Reference-free SNP calling: improved accuracy by preventing incorrect calls from repetitive genomic regions

Biology Direct

Table 1 Summary of two real sequencing datasets used for evaluation of the iML algorithm

	Arabidopsis thaliana	Gasterosteas aculeatus
Library preparation	2b-RAD	RAD
Restriction enzyme	BsaXI (ACN₅CTCC)	SbfI (CCTGCAGG)
Trimmed read length	27 bp	55 bp
High-quality reads	5,845,509	4,672,098
Mapped reads	5,339,662	4,139,761
Clustered reads	5,809,558	4,220,881
No. of in silico restriction sites^a	39,678	45,600
No. of in silico unique sites	35,362	40,125
No. of read clusters	33,877	42,352
Reference	[9]	[10]

^a, the total number of restriction sites that were predicted from the genome assemblies of TAIR8 and BROADS1 for A. thaliana and G. aculeatus, respectively.

ISSN: 1745-6150